I've never canvassed over a whole transom. Always left them bright. I suppose if I did canvas over the transom, I would do that first.
I canvas the hull upside down on horses just like with any canoe with a come along.
Stretch and Staple at the gunwales, finish off the bow, then put "cheater" staples around the transom to hold the stretch.
Cut it free and finish the final attachment to the transom, whether you make a fold to double it and staple it to the hull, flush with the transom or pull it over the transom and attach directly.
With the doubling fold, be sure to put bedding compound between the flood and the wood.
When pulling the canvas over and attaching directly to the transom face, I make trim to cover where it is stapled.
Hard to describe with out photos... I'll see if I can find some that help this make sense...
Sorry for the upside down photos....they are right side up when I uploaded them...